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  • Articles
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    • COVID-19 Research and News from ASM Journals
    • mSphere of Influence: Commentaries from Early Career Microbiologists
    • Archive
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Applied and Environmental Science

  • Open Access
    Modifying <span class="named-content genus-species" id="named-content-1">Saccharomyces cerevisiae</span> Adhesion Properties Regulates Yeast Ecosystem Dynamics
    Research Article | Applied and Environmental Science
    Modifying Saccharomyces cerevisiae Adhesion Properties Regulates Yeast Ecosystem Dynamics

    The impact of direct (physical) versus indirect (metabolic) interactions between different yeast species has attracted significant research interest in recent years. This is due to the growing interest in the use of multispecies consortia in bioprocesses of industrial relevance and the relevance of interspecies interactions in establishing stable synthetic ecosystems. Compartment bioreactors have traditionally been used in this regard...

    Debra Rossouw, Skye P. Meiring, Florian F. Bauer
  • Open Access
    Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products
    Research Article | Applied and Environmental Science
    Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products

    Validated methods are urgently needed to improve DNA sequence-based assessments of complex bacterial communities. In this study, we used 16S rRNA PCR amplicon and gDNA mock community standards, consisting of nine, dairy-associated bacterial species, to evaluate the most commonly applied 16S rRNA marker gene DNA sequencing and analysis platforms used in evaluating dairy and other bacterial habitats. Our results show that bacterial...

    Zhengyao Xue, Mary E. Kable, Maria L. Marco
  • Open Access
    Biofilm Formation Drives Transfer of the Conjugative Element ICE<em>Bs1</em> in <em>Bacillus subtilis</em>
    Research Article | Applied and Environmental Science
    Biofilm Formation Drives Transfer of the Conjugative Element ICEBs1 in Bacillus subtilis

    Transfer of mobile genetic elements from one bacterium to another is the principal cause of the spread of antibiotic resistance. However, the dissemination of these elements in environmental contexts is poorly understood. In clinical and environmental settings, bacteria are often found living in multicellular communities encased in a matrix, a structure known as a biofilm. In this study, we examined how forming a biofilm influences the...

    Frédéric Lécuyer, Jean-Sébastien Bourassa, Martin Gélinas, Vincent Charron-Lamoureux, Vincent Burrus, Pascale B. Beauregard
  • Open Access
    Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River
    Research Article | Applied and Environmental Science
    Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River

    Landfill leachate is a persistent contamination threat for terrestrial waters. Microbial metabolism in landfills transforms contaminants and contributes to greenhouse gas emissions. A better understanding of landfill-associated microbial communities will inform bioremediation of solid waste environments and improve pathogen monitoring. We leveraged shotgun metagenomics to investigate the microbial communities of the Riverton City dump...

    Aneisha M. Collins-Fairclough, Rebecca Co, Melessa C. Ellis, Laura A. Hug
  • Open Access
    Complete Genome Sequence of a <em>bla</em><sub>KPC-2</sub>-Positive <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan
    Research Article | Applied and Environmental Science
    Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan

    We isolated and determined the complete genome sequence of a KPC-2-producing K. pneumoniae strain from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP). In Japan, the KPC type has been very rarely detected, while IMP is the most predominant type of carbapenemase in clinical carbapenemase-producing Enterobacteriaceae (CPE) isolates...

    Tsuyoshi Sekizuka, Koji Yatsu, Yuba Inamine, Takaya Segawa, Miho Nishio, Norimi Kishi, Makoto Kuroda
  • Open Access
    The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in <span class="named-content genus-species" id="named-content-1">Pseudomonas putida</span> KT2440
    Research Article | Applied and Environmental Science
    The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in Pseudomonas putida KT2440

    The function of lanthanides for methanotrophic and methylotrophic bacteria is gaining increasing attention, while knowledge about the role of rare earth elements (REEs) in nonmethylotrophic bacteria is still limited. The present study investigates the recently described differential expression of the two PQQ-EDHs of P. putida in response to lanthanides. We demonstrate...

    Matthias Wehrmann, Charlotte Berthelot, Patrick Billard, Janosch Klebensberger
  • Open Access
    A Population-Based Surveillance Study of Shared Genotypes of <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Isolates from Retail Meat and Suspected Cases of Urinary Tract Infections
    Research Article | Applied and Environmental Science
    A Population-Based Surveillance Study of Shared Genotypes of Escherichia coli Isolates from Retail Meat and Suspected Cases of Urinary Tract Infections

    Community-acquired urinary tract infection caused by Escherichia coli is one of the most common infectious diseases in the United States, affecting approximately seven million women and costing approximately 11.6 billion dollars annually. In addition, antibiotic resistance among E. coli bacteria...

    Reina Yamaji, Cindy R. Friedman, Julia Rubin, Joy Suh, Erika Thys, Patrick McDermott, Melody Hung-Fan, Lee W. Riley
  • Open Access
    Direct Detection of Carbapenem-Resistant Organisms from Environmental Samples Using the GeneXpert Molecular Diagnostic System
    Observation | Applied and Environmental Science
    Direct Detection of Carbapenem-Resistant Organisms from Environmental Samples Using the GeneXpert Molecular Diagnostic System

    Use of the Carba-R assay for detection of carbapenem-resistant Gram-negative organisms (CROs) can provide data for implementation of a rapid infection control response to minimize the spread of CROs in the health care setting.

    K. A. Perry, J. B. Daniels, S. C. Reddy, A. J. Kallen, A. L. Halpin, J. K. Rasheed, J. A. Noble-Wang
  • Open Access
    Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community
    Research Article | Applied and Environmental Science
    Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

    Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge...

    Adit Chaudhary, Imrose Kauser, Anirban Ray, Rachel Poretsky
  • Open Access
    A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection
    Research Article | Applied and Environmental Science
    A Reference Viral Database (RVDB) To Enhance Bioinformatics Analysis of High-Throughput Sequencing for Novel Virus Detection

    To facilitate bioinformatics analysis of high-throughput sequencing (HTS) data for the detection of both known and novel viruses, we have developed a new reference viral database (RVDB) that provides a broad representation of different virus species from eukaryotes by including all viral, virus-like, and virus-related sequences (excluding bacteriophages), regardless of their size. In particular, RVDB contains endogenous nonretroviral...

    Norman Goodacre, Aisha Aljanahi, Subhiksha Nandakumar, Mike Mikailov, Arifa S. Khan

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